Re: [gmx-users] D-amino acids' force fields

; > > Best regards, > > > Mijiddorj > > -- > > Message: 5 > Date: Sat, 22 Oct 2016 10:11:50 +0200 > From: Tsjerk Wassenaar > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] D-amino acids' force fields &g

Re: [gmx-users] D-amino acids' force fields

Hi Mijidorj, These amino acids are chemically and topologically equivalent to their L counterparts. For united atom force fields you only need to invert the improper dihedral at the C-alpha. For atomistic force fields you don't need to change anything, except the CMAP stuff in Charmm for the backb

Re: [gmx-users] g_membed failure

Hi Sophia, I can't help out with mdrun -membed, but I did write a tool (insane) to avoid just the hassle you seem to face. It builds a coarse grained system, but that can be converted to atomistic. Depending on what exactly you need to do, it may be trivial or less so. In either case, if you care,

Re: [gmx-users] principal component analysis chain break (Tsjerk Wassenaar)

_gmx-users digest..." > > > > > > Today's Topics: > > > >1. Umbrella sampling tutorial (gozde ergin) > >2. principal component analysis chain break (??) > >3. Re: principal component analysis chain break (Tsjerk Wassenaar) > > &g

Re: [gmx-users] principal component analysis chain break

Ni hao Jie, The extreme projections are typically pretty meaningless. But if you want them or the more meaningful PCA output, do make sure you remove jumps over PBC from your input trajectory and have the molecules whole/clustered. Cheers, Tsjerk On Oct 7, 2016 11:21 AM, "胡杰" wrote: > Dear Gr

Re: [gmx-users] RMSD of energy minimized structure

Hi Surya, The first part ss a warning, not an error. It also says (implicitly) that if the molecules are not broken across PBC then there's nothing to worry about whatsoever. So just assert that your molecules are not split over PBC. Have a look at the trajectory. If there are frames with one part

Re: [gmx-users] question

Hi Alvaro, gmx genconf Hope it helps, Tsjerk On Sep 29, 2016 4:59 PM, "ÁLVARO RODRIGO RUIZ FERNÁNDEZ" < arr...@ug.uchile.cl> wrote: > Dear gromacs users: > > How I can multiply a box full of molecules from 1x1 to 2x2 ?, I know I can > use Avogadro but in this case it does not work, I think fo

Re: [gmx-users] Cluster Analysis

Hi Sanket, gmx trjconv allows writing frames based on a frame index file or using a xvg file and threshold. Check the help of trjconv on it. Hope it helps, Tsjerk On Thu, Sep 29, 2016 at 9:05 AM, Sanket Ghawali wrote: > Dear, gmx-users, > > I performed a cluster analysis using gmx cluster. I

Re: [gmx-users] Problem in PCA of protein ligand system

t motions of only ligand, along a particular > direction (say rotation along a dihedral in ligand) from this trajectory? > > Best Regards > Ashutosh > > On Mon, Sep 26, 2016 at 3:52 PM, Tsjerk Wassenaar > wrote: > > > Hi Ashutosh, > > > > To simplify this,

Re: [gmx-users] Problem in PCA of protein ligand system

Hi Ashutosh, To simplify this, let's do PCA of two balls on opposite ends of a stick I'm rotating. The mean position of both ends is right at the center of rotation, and the relative positions I can describe with X and Y coordinates only. Now, the essence of PCA is the question 'which single direc

Re: [gmx-users] Large (600k particle) semi-isotropic lipid bilayer system transformed into vacuum-separated coordinates by grompp and mdrun

Hi George, Oh, quadrants over PBC, so it just completely ruptured. It means the area per lipid is really off in your starting structure. Where did you get it from? Cheers, Tsjerk On Sep 8, 2016 3:54 PM, "George Pantelopulos" wrote: > Dear Tsjerk and Erik, > > Thank you for the responses! > >

Re: [gmx-users] Large (600k particle) semi-isotropic lipid bilayer system transformed into vacuum-separated coordinates by grompp and mdrun

Hi George, How did you build the starting structure? The quadrants are due to distribution over cores/nodes. You can try EM on a single core for a few steps, but it seems that the system is too stretched anyway, so I think that won't really solve your problem. Cheers, Tsjerk On Sep 7, 2016 11:

Re: [gmx-users] Odd behaviour of editconf or VMD?

Hi Jernej, This is simpler in two dimensions: Consider a hexagonal unit cell. Draw it, together with the surrounding copies (7 hexagons total). Now connect the central hexagon with the right horizontal neighbor, and with the 'northeast' neighbour. Connect these two neighbors with their other commo

Re: [gmx-users] X Amino Acids for Building CG Structure

Hi Elka, Methyl asparagine is not known by DSSP and is not availble in Martini. You're probably best off replacing it by asparagine: sed '/^ATOM/s/MEN/ASN/' 1HG0.pdb > out.pdb Cheers, Tsjerk On Fri, Aug 26, 2016 at 11:26 AM, Elka Firmanda wrote: > Hi, I just got "X" amino acids on DSSP, what

Re: [gmx-users] COM-COM distance: PBC problem

Hi Arnost, When you fit with rotation the coordinates and the box are not on par anymore. Anything you do after that tries using PBC will fail. I guess that Plumed is trying to use the box to get the COM-COM distance. The only (practical) solution: don't fit. Cheers, Tsjerk On Aug 17, 2016 00:2

Re: [gmx-users] Box dimensions variation

Hi Yasser, Probably you're using semi-isotropic pressure coupling, which you should only do if you have a membrane like structure aligned with the XY plane (or a somewhat stiffish wire like structure aligned along z). Cheers, Tsjerk On Wed, Aug 10, 2016 at 3:52 PM, Yasser Almeida Hernández < ya

Re: [gmx-users] Preparing 30% TFE/Water simulation

Hi Sanket, That's not really a Gromacs question, is it? And it's pretty simple math, once you decide what you mean with 30%. You may want to check https://en.wikipedia.org/wiki/Concentration Cheers, Tsjerk On Fri, Jul 29, 2016 at 7:44 AM, Sanket Ghawali wrote: > Dear, gmx-users, > > Hello eve

Re: [gmx-users] Magic number error in XTC file

Hi Gayathri, For the XTC file you used only a selection of atoms to write out. The TRR file always contains everything. With the conversion from TRR to XTC make sure to write the same selection as is in the other XTC files. Hope it helps, Tsjerk On Thu, Jul 28, 2016 at 7:36 AM, GAYATHRI S wrot

Re: [gmx-users] Cutting simulatio box

etween 'single' molecule at specific 'z' of the box > indicating the phases . > > So I think my given way is easier, but not sure if the reruns goes like the > original simulations? > > > Best regards > > > On Mon, Jul 18, 2016 at 12:57 PM, Tsjerk Wa

Re: [gmx-users] Cutting simulatio box

Hi Faezeh, You could use gmx select to make groups for the two phases and then perform a rerun with these new groups as energy_grps. That would give you the within and between group energies. Hope it helps, Tsjerk On Jul 18, 2016 12:49 PM, "Faezeh Pousaneh" wrote: Hi, I have a Phase-separati

Re: [gmx-users] Facing poblem in enegy minimization step

e > either the topology is bad or the starting structure has clashes that > cannot be adequately addressed using EM or because of improper > parametrization. > > > On Sat, Jul 16, 2016 at 3:43 PM, Tsjerk Wassenaar > wrote: > > > Hi Swagata, > > > > That's

Re: [gmx-users] Facing poblem in enegy minimization step

Hi Swagata, That's not a problem. You should be fine running a simulation, given the potential energy of the system. Check the archives for more elaborate comments on this matter. And please check the archives/google before posting questions. We like breaking our heads over new, tough issues, and

Re: [gmx-users] System blowing up in final MD run

Hi Deep, What force field? What system? How many cores? Did you try running on one? What error? Did pdb2gmx or grompp give any warnings? Cheers, Tsjerk On Wed, Jul 13, 2016 at 5:44 AM, Deep Bhattacharya wrote: > Hello, > My system is blowing up for the protein carbohydrate solvent complex. I

Re: [gmx-users] How to solvate particular regions in simulation box

Hi Venkat, First, note that there are no such things as hollow ('vacuum-filled' :p) proteins in nature. Simulating a capsid without contents is probably non-sensical. Besides that, you could try insane (http://cgmartini.nl/index.php/insane). By default it excludes the inside of a protein for place

Re: [gmx-users] Position restraints for water during EM

Hi Gregory, There is no default position restraint during EM. Of course, one wouldn't expect them to move much and one would expect the local energy minimum to be rather close to the initial position, if you used an equilibrated water box to set up the system. Cheers, Tsjerk On Jul 8, 2016 08:38

Re: [gmx-users] PCA and gmx analyze

Hi Suniba, Don't look at the cosine content. It doesn't convey anything useful. If you want to know more, I've posted more lengthy remarks about it before. Cheers, Tsjerk On Jun 27, 2016 1:11 PM, "Sun Iba" wrote: > Hello Users and experts > > My system details: > Force field: GROMOS 43a1 > > G

Re: [gmx-users] wrap only in XZ?

Hi Albert, Rotate the system 90 degrees and use PBC in xy only. Cheers, Tsjerk On Jun 26, 2016 9:04 AM, "Albert" wrote: > Hello: > > I've got a membrane protein system and I would like the water and ions > only wrap in XZ direction. Currently, they can also wrap at Z direction. I > am just won

Re: [gmx-users] least-squares fitting the second structure on the reference structure

Hi Qasim, If you fit a trajectory, with trjconv -fit rot+trans, then each frame is fit onto the reference. Hope it helps, Tsjerk On Tue, Jun 21, 2016 at 11:12 AM, Qasim Pars wrote: > Dear users, > > From GROMACS online manual: > gmx confrms computes the root mean square deviation (RMSD) of tw

Re: [gmx-users] Insufficient memory (128 GB) for ensemble entropy calculation with gmx covar/gmx anaeig

Hi David, And why the number of frames? Cheers, Tsjerk On Tue, Jun 21, 2016 at 9:52 AM, David van der Spoel wrote: > On 21/06/16 09:40, Qasim Pars wrote: > >> Dear David, >> >> Could you please more explain each term of the formula you said? >> >> Formula=The number of atoms (N * 3)^2 times n

Re: [gmx-users] SOLVED: Re: helixorient, jacobi iteration or junk output...?

Hi Phil, Did you write all atoms to the trajectory or only a group? Does the reference structure match the trajectory? The Jacobi error usually occurs when there is a mismatch, and the route via a PDB file is consistent with that. Cheers, Tsjerk On Sat, Jun 18, 2016 at 3:25 AM, Phil Dude wrote

Re: [gmx-users] Calculating Eccentricity

Hi Sanket, You probably want the clustering routine of trjconv. And then calculate the principal axes of the micelle. The instantaneous value does not mean much, but a an average non-zero eccentricity would suggest with a greater extent than without peptide would suggest an effect. Note that you d

Re: [gmx-users] to neutralize the system

Hi Qasim, Not only should you neutralize the system, but you should add additional ions too. The behaviour of charged side chains which can find a partner ion from solution is different from those that can't. You won't see any problems, but the results will be affected. Not coming across any probl

Re: [gmx-users] Is charmm GUI ideal for membrane building

upposed to converge. Maybe you want > to verify something else? > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Tsjerk > Wassenaar > Sent: Monday,

Re: [gmx-users] Is charmm GUI ideal for membrane building

Hi Amit, What membrane and what time scale are you talking about? Complex membranes may take microseconds to equilibrate. Cheers, Tsjerk On Jun 13, 2016 06:13, wrote: > Hello everyone, > I built a lipid membrane in Charmm-GUI and tried to equilibrate it in > GROMACS 5.1.2. But the total energy

Re: [gmx-users] How many times should I do Umbrella Sampling

Hi Agnivo, In addition to the remarks of Andre, if you can show that another US run on the same system gives pretty much the same result, then you can present that as proof of the robustness, and it is futile to do three more, especially if you have convergence and sufficient overlap. You can high

Re: [gmx-users] Saving time of the coordinates for conformational entropy

Hi Qasim, The RMSD is not good for assessing convergence, especially if it goes above 0.5 nm. Cheers, Tsjerk On Wed, Jun 8, 2016 at 8:48 PM, Qasim Pars wrote: > Dear users, > > I have simulated a protein with simulation time of 200 ns and saving the > coordinates at every 40 ps. Conformation

Re: [gmx-users] PCA problems

Hey :) > That usually gives a fitted ensemble that more closely retains the > original RMSD values between all pairs of structures. > This should read: ... a fitted ensemble of which the sum of the traces of all pairwise inner product matrices is closer to minimal. The pairwise RMSDs (and thei

Re: [gmx-users] PCA problems

Hi James, That's silly! Ambiguous means that the same structure can have multiple solutions in a fit. The fit to a single reference structure (with more than three atoms) is never ambiguous. Can never, by definition! Now if you have two reference structures at hand, and they have (quite) differen

Re: [gmx-users] RMSD question

Hi Teresa, You probably want to try clustering, and then check the percentage of bound/unbound structures in the clusters you get. Just the RMSD won't tell you much. Cheers, Tsjerk On Wed, Jun 8, 2016 at 11:30 AM, ingram wrote: > Dear GROMACS community, > > I am trying to identify the number

Re: [gmx-users] PCA problems

Hi James, 'Spurious alignment' is the dependence of the resulting ensemble on the reference structure. Unfortunately, that's not solved by a progressive fit. Rather, in a progressive fit, the same configuration can have multiple orientations, based on the previous structures, which is also problem

Re: [gmx-users] PCA problems

Hi Teresa, No, the peptide should not be broken. Did you remove jumps over PBC? The peptide will probably be severely distorted by filtering, though. Cheers, Tsjerk On Wed, Jun 8, 2016 at 8:49 AM, ingram wrote: > Dear GROMACS community > > I am trying to complete a PCA analysis of my peptide

Re: [gmx-users] Simulating a protein dimer

Hey :) There's a suggested workflow on the Gromacs site: http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Cheers, Tsjerk On Jun 7, 2016 11:50 PM, wrote: > I solved the problem by using an em.tpr with pbc nojump for my dimers. pbc > whole takes the monomers as whol

Re: [gmx-users] projection on the first two eigenvectors obtained from the concatenated trajectories

I couldn't find anything about that on google. > > Cheers, > > On 7 June 2016 at 15:15, Tsjerk Wassenaar wrote: > > > Hi Qasim, > > > > What makes you think that they should start at 0,0 ? > > The overall mean of any set of projections lies at the origi

Re: [gmx-users] DPPC-DOTAP Mixed Lipid Bilayer

Hi Nidhin, It looks like you have a version of insane that still builds oleyl with five beads. It should be four as 'CDCC' like you did for building the topology. So you also need to remove the C5 beads and shift the D to position two. Then you should be set to make/simulate your bilayers. Cheers

Re: [gmx-users] DPPC-DOTAP Mixed Lipid Bilayer

t; structure (Md. Imrul Reza Shishir) > > 2. cannot output all the structures of one cluster (Zhenyu Meng) > > 3. Re: Non-bonded energy (ABANTIKA PAL) > > 4. Re: gmx gangle selections help (Teemu Murtola) > > 5. Re: DPPC-DOTAP Mixed Lipid Bilayer (Tsjerk Was

Re: [gmx-users] Dodecahedron Box size and Appropriate number of SOL molecules

Hi Apramita, No restrictions. You're in charge. To get a correct density, you'll need to equilibrate with pressure coupling. Cheers, Tsjerk On Tue, Jun 7, 2016 at 1:08 PM, Apramita Chand wrote: > Hey, > Thanks a lot Tsjerk for your advice regarding box size. You've mentioned > that we coul

Re: [gmx-users] projection on the first two eigenvectors obtained from the concatenated trajectories

Hi Qasim, What makes you think that they should start at 0,0 ? The overall mean of any set of projections lies at the origin. PCA is a pretty powerful and advanced technique, that requires quite a bit of thinking in the preparation, the execution and the interpretation. Please do read plenty of tu

Re: [gmx-users] Fwd: Dodecahedron Box size and Appropriate number of SOL molecules

Hi Apramita, First of all, your box diameter should be the length of the peptide plus 2, with a minimum of 2.8. Otherwise, the peptide will be able to interact directly with its periodic image. The solvent is typically added by overlaying a box of pre-equilibrated solvent and deleting all molecul

Re: [gmx-users] DPPC-DOTAP Mixed Lipid Bilayer

Hi Nidhin, Insane allows you to build lipids from the command line. Alternatively, it's pretty easy to add DOTAP to insane, using the templates inside. If you feel you need a hand with that, let me know. Cheers, Tsjerk On Jun 7, 2016 12:21 AM, "Nidhin Thomas" wrote: > Hi GROMACS Users, > > I w

Re: [gmx-users] error installing trj_cavity with gromacs

Hi Williams, It looks like you didn't set the Gromacs include directory. What command/procedure did you use to compile? Cheers, Tsjerk On Jun 3, 2016 21:25, "Williams Miranda" wrote: > Dear GROMACS users > I use gromacs 4.6.5, then, I downloaded trj_cavity v1.1 for installation. > But I am get

Re: [gmx-users] allosteric effect

Hi Qasim, Do you assume MWC or KNF like allostery, and conformational based, dynamics based or mixed? Cheers, Tsjerk On Fri, Jun 3, 2016 at 2:54 AM, Qasim Pars wrote: > Dear gmx users, > > The protein I have simulated over 200 ns with GROMACS is dimer and shows > positive allostery. Based on

Re: [gmx-users] Cross correlation map of residues

Hi Qasim, The plot you refer to is the result of NMA on C-alpha only. So g_covar -xpma using only C-alpha atoms should come close. You might also want to try the g_correlation tool mentioned earlier on the list, but again with a selection of only C-alpha atoms. Cheers, Tsjerk On Fri, Jun 3, 201

Re: [gmx-users] protonation of histidines

Hi Irem, pdb2gmx checks the hydrogen bonding network and decides which form of His fits best. Cheers, Tsjerk On Jun 2, 2016 17:20, "Irem Altan" wrote: > Hi, > > When I process a .pdb structure using pdb2gmx, how does Gromacs add > hydrogens to the histidine residues? I see that in the processe

Re: [gmx-users] NMA problems with mass-weighting -m option

Hi Riccardo, The boolean options are specified as -m or -nom, without further arguments. For non-mass-weigthed you want -nom. Hope it helps, Tsjerk On May 27, 2016 15:49, "Ravasio Riccardo" wrote: > Dear gmx users, > > > After performing Normal Mode Analysis, I would like to print a non > mass

Re: [gmx-users] Using pdb2gmx with martini (coarse-grained) model to assign termini charges

Hi Sourav, For Martini there's the conversion script martinize, which has an option -nt to suppress putting charges on termini. This is not really a Gromacs question, and it's better to post Martini related questions on the forum at http://cgmartini.nl Cheers, Tsjerk On May 24, 2016 23:35, "Jus

Re: [gmx-users] find out tpx version of tpr

Hey :) If you just have the .tpr and you don't want to use Gromacs' tools, you can use python: python -c 'import struct; print "".join(struct.unpack(100*"c",open("YOUR-TPR-HERE").read(100)))' (Python 2, mind you). Cheers, Tsjerk On Mon, May 23, 2016 at 11:33 AM, Mark Abraham wrote: > Hi, >

Re: [gmx-users] g_cluster analysis

Hi Sapna, How should we know how many clusters you should have? A cutoff of 0.2 is quite tight, and will give many clusters. Whether that's what you want/need or whether that's meaningful/helpful for your goals is something you should consider. We don't know what you're trying or doing. Cheers,

Re: [gmx-users] WARNING no output error while dumping structures with trjconv from MD.trr

Oh, you don't want to dump one frame! You want the frames beyond 25 ns. So don't use -dump at all. You'll only get one frame though, using a spacing of 1 ns. Cheers, Tsjerk On May 21, 2016 13:53, "Tsjerk Wassenaar" wrote: > Hi Antara, > > You indicate you w

Re: [gmx-users] WARNING no output error while dumping structures with trjconv from MD.trr

Hi Antara, You indicate you want the frame at 27ns (-dump 27000), but that's not in the trajectory. The suggestion is to ask for a frame that is in, like -dump 25290 Cheers, Tsjerk On May 21, 2016 13:09, "Antara mazumdar" wrote: Dear gromacs users, I was trying to dump structures from MD.t

Re: [gmx-users] simulation_time[Nikita Bora]

Hi Nikita, It's not like there's a range to take a minimum from. It's this with this force field and that with another. Any deviation will alter the behaviour of the force field, and you'll have to show that the result is valid, either by running tests, or by referring to a paper that has results

Re: [gmx-users] Help required for calculation of protein coverage % wrt time

Hi Antara, You can also simply calculate the ratio of buried surface area to total surface area, which you can both get with gmx sasa Cheers, Tsjerk On Thu, May 19, 2016 at 3:10 PM, Sarath Chandra < sarathchandrada...@gmail.com> wrote: > You can use g_contacts tool which will give you list of

Re: [gmx-users] simulation_time

Hi Nikita, That's actually a good question, and I think it hasn't been phrased like this before. I rephrase it slightly again, so it says "which parameters should be considered part of a force field?" The first thing that springs to mind is not really a parameter, but a vital part of the force fi

Re: [gmx-users] Production run error

Hi Sanket, The problem is that a charge group moved too far between two domain decomposition steps. Seriously, we can't say more than that, unless you tell us more about the system and how you got to the point where you are. Cheers, Tsjerk On May 18, 2016 8:44 AM, "Sanket Ghawali" wrote: > *D

Re: [gmx-users] Calculating Distance

Hi Sanket, You can use 'gmx traj' to write the COM over time. Cheers, Tsjerk On Wed, May 18, 2016 at 7:09 AM, Sanket Ghawali wrote: > Thank you Justin. I am sorry, I didn't make my query specific. > > g_dist calculates distance between COMS of 2 groups with reference to time. > I want to moni

Re: [gmx-users] Removing periodic boundary condition

Hi Sanket, Can you check the structure in the tpr file (editconf -f .tpr -o .gro/.pdb)? If that is good, then -pbc nojump should work. For the second pass, you shouldn't need -pbc mol then. Cheers, Tsjerk On May 16, 2016 9:06 AM, "Sanket Ghawali" wrote: > Dear, gmx-users, > > Hello everyone, >

Re: [gmx-users] PCA and FEL

o variables with free energy? like > RMSD and Rg? > > > Sent from my iPhone > > > On 15-May-2016, at 10:51 am, Tsjerk Wassenaar wrote: > > > > Hi Suniba, > > > > No, with gmx anaeig you can select -2d, which does a 2D projection onto > the > &

Re: [gmx-users] PCA and FEL

Hi Suniba, No, with gmx anaeig you can select -2d, which does a 2D projection onto the selected eigenvectors. Alternatively, you can combine any two projections onto eigenvectors, which you get using the option -proj. The quickest way to do that is something like: paste <(grep -v '^[@#]' proj1.x

Re: [gmx-users] (no subject)

Hi Upasana, What is your goal, your research objective? 'opening it for docking purpose' is way too vague for us to help you, other then suggesting that you are probably not choosing an optimal approach. Cheers, Tsjerk On May 14, 2016 07:04, "Upasana Ray" wrote: > Dear user, > > I have gener

Re: [gmx-users] LINCS WARNING Error in running production run in parallel of a MARTINI SYSTEM of membrane protein

Hi Antara, What commands did you use? At least make sure you add -rdd 1.6 to the command line of mdrun, because the default value is too small for coarse grain simulations. Cheers, Tsjerk On Fri, May 13, 2016 at 8:12 PM, Antara mazumdar wrote: > Dear users, > > I am trying to run a coarse gra

Re: [gmx-users] Higher Density than Expected

Hey :) Salt water has a higher density than pure water anyway. Cheers, Tsjerk On Apr 26, 2016 5:19 PM, "Christopher Schlicksup" wrote: > Thanks Justin. I was expecting closer to 1000kg/m^3. My reading about the > tip3p water model found approximately this value at 300K, and it is also > the ap

Re: [gmx-users] Standard volume of the simulation box

Hi Sana, There's no such thing as a standard volume. The key decision you have to take is what distance there should be between periodic images, for which the consensus view is that you need at least 2.0 nm. I typically use 2.25, corresponding roughly to 9 layers of water, so the protein can stret

Re: [gmx-users] Catenation and Visualization

Hi Suniba, For the first part, look up 'periodic boundary conditions' (my oh my, there should be a keyboard shortcut for that term). For the second part, it seems you have loaded two files, and you should see two objects in the right side panel of Pymol. You can turn visualization off by clicking

Re: [gmx-users] question about preferred values in itp files

Hey, In addition, for Q3, sure you can have a program build you acetonitrile from the interactions. But what about cholesterol? Morphine? A protein? For just a bit more complicated stuff, let alone the really complicated stuff, you need to have coordinates to start with. Cheers, Tsjerk On Apr 14

Re: [gmx-users] very strange phenomenon for my production MD by gromacs

right! Cheers, Tsjerk On Apr 14, 2016 05:32, "Brett" wrote: > Dear All, > > If the issue in my production MD was caused by > "Periodic_Boundary_Conditions", I can continue my production MD until it > completed, and it will not affect my final results suppose I have it > corrected by trjconv, ri

Re: [gmx-users] EM replicates

Hi Gregory, Yes, these steps are deterministic. Think of where the randomization should come from. Sure, there is 'random' placement of ions in genion, but it has a default seed, resulting in deterministic random numbers :) Hope it helps, Tsjerk On Apr 9, 2016 00:33, "Gregory Poon" wrote: > He

Re: [gmx-users] Partial density versus time

s. This could be easily done by g_density with an .ndx file. I need > to > > have a plot of density-time for each of the components of the system. > > > > Please help... > > > > > > > > > > Best regards > > > > > > On Wed, Apr 6, 2016 at

Re: [gmx-users] Partial density versus time

> > Best regards > > > On Wed, Apr 6, 2016 at 4:58 PM, Tsjerk Wassenaar > wrote: > > > Hi Faezeh, > > > > Using -b/-e flags you can get the density profile over a window of time > (or > > a single frame). Afterwards you can combine the results to h

Re: [gmx-users] Partial density versus time

Hi Faezeh, Using -b/-e flags you can get the density profile over a window of time (or a single frame). Afterwards you can combine the results to have a density profile over time. Hope it helps, Tsjerk On Wed, Apr 6, 2016 at 4:29 PM, Faezeh Pousaneh wrote: > Hi, > > Is it possible to obtain p

Re: [gmx-users] appropriate position restraint for stability of alpha helix

Hi Mijiddorj, For a biologically stable alpha-helix, you should not use any restraints. If you want to stabilize a helix that is known to fold/unfold, then try something not too stiff. Usually like 100 kJ/mol/nm^2 should already do. But again, don't try to 'fix' a force field in this way. Cheers,

Re: [gmx-users] simulation a box of water

Hi Saeed, Us a larger box, like edge length 2.5 or 3. The non-matching names are not much of a problem, and you can add -maxwarn 1 to the grompp call. Cheers, Tsjerk On Apr 2, 2016 8:29 AM, "Saeed Nasiri" wrote: > thank you TsjerkI modified the topology file and did all the thing from the > be

Re: [gmx-users] simulation a box of water

Hi Saeed, Just before [ molecules ] insert the lines: [ system ] A box of water Cheers, Tsjerk On Apr 2, 2016 8:06 AM, "Saeed Nasiri" wrote: > Dear users > > I have constructed a box of only water molecules, but I don't know how to > constructed the topology file. I wrote this file but it did

Re: [gmx-users] is it necessary to mdrun posre_npt.mdp first and then posre_nvt.mdp

No, what Mark means is that if you equilibrated temperature AND pressure (NpT) there's no point in an NVT step, in which the pressure may go off again, even though it's unlikely to matter much, because the volume is already within proper range. However, there's the 'posre' part still, which sugges

Re: [gmx-users] -pbc nojump failure

: > You could try to fit first (-fit rot+trans) and fix pbc (-pbc nojump) > later. > > Cheers, > > Fra > > On 31 March 2016 at 05:45, Tsjerk Wassenaar wrote: > > > Hi Irem, > > > > Check the structure in nvt_water_frozen.tpr: > > > > gmx editco

Re: [gmx-users] Generate diagram/figure with information about protein-ligand interactions

Hi biohpc, For this you need to combine output from gmx hbond, gmx sasa, and gmx saltbr. Cheers, Tsjerk On Mar 31, 2016 12:58, "bio hpc" wrote: > My problem is not excel or whatever graphical program. I just need the > data, in an automatic way. Then I can use either matplotlib or similar to >

Re: [gmx-users] -pbc nojump failure

Hi Irem, Check the structure in nvt_water_frozen.tpr: gmx editconf -f nvt_water_frozen.tpr -o ref.pdb Cheers, Tsjerk On Mar 31, 2016 00:04, "Irem Altan" wrote: > Hi, > > I am simulating a protein in its unit cell. I use the original .pdb file > as an input, so the initial molecule is not frag

Re: [gmx-users] Use pdb file generated with Maestro, in Gromacs

Hey :) -ignh does ignore the hydrogens in the input file. It builds those hydrogens that are specified in the force field. For histidines, the protonation state is determined from the possible hydrogen-bonded network, but it is possible to assign specific states interactively, using the option -hi

Re: [gmx-users] on the gromacs force field for keep helix

Hi Brett, There is no GROMACS force field. Now the original GROMOS force fields 53a5 and 53a6 are known to be more unstable in the helix department than they should, so better not use those. There are newer versions of 53a6 and there's 54a7, which are fine. I'm actually not entirely sure what vers

Re: [gmx-users] unit cell vector warning

Hi Irem, The correction vectors is internal bookkeeping stuff, making sure to keep track of what is where in a computationally efficient manner. To get rid of this, I think the best option is to rotate your unit cell, to have the largest vector (your third) along the x-axis. The second largest sh

Re: [gmx-users] elastic restraints in MARTINI simulation

> > > the correct choise influence on sampling here`? E.g in full atomistic > > > sims generally langevens dynamics produces better results in > > > comparison to berendsen thermostat which produce very unphysical > > > behaviour for the macromolecular systems. > &g

Re: [gmx-users] elastic restraints in MARTINI simulation

sjerk, does it make sense to try to have grompp observe the particle > density and guide the default of -rdd accordingly? > > Mark > > On Wed, Mar 23, 2016 at 9:19 AM Tsjerk Wassenaar > wrote: > > > Hi James, > > > > Try setting -rdd 1.4 in mdrun. Sometimes 1.5 or

Re: [gmx-users] elastic restraints in MARTINI simulation

Hi James, Try setting -rdd 1.4 in mdrun. Sometimes 1.5 or 1.6 is necessary (especially if you use a larger time step, like 30 fs). Cheers, Tsjerk On Mar 23, 2016 09:08, "James Starlight" wrote: > Hello, > > > I am trying to perform 2 MARTINI simulations of several membrane > receptors within m

Re: [gmx-users] creating representative structures

Hi Shyno, Is there a difference in mass-weighting? Can you try on C- alphas only? Cheers, Tsjerk On Mar 16, 2016 15:55, "Shyno Mathew" wrote: > Dear all, > > > I wrote a tcl script to do cluster analysis, using gromos method. My > results are slightly different from the g_cluster results. I se

Re: [gmx-users] Volume and boundary Questions

Hey :) You can define any box 'shape', expressed in terms of the corresponding lattice vectors, compliant with the rules stated in chapter 3 of the manual. You can set a hexagonal prism cell using editconf, using the -box and -angles options. In your case, the long edge should be along x, and has

Re: [gmx-users] creating representative structures

Hi Stephane, The difference is too large for rounding errors. I was not suggesting different selections, but rather mass-weighting versus non-mass-weighting. Cheers, Tsjerk On Mar 17, 2016 23:15, "Téletchéa Stéphane" < stephane.teletc...@univ-nantes.fr> wrote: > Le 16/03/2016 16:54, Shyno Mathe

Re: [gmx-users] Reconstruction of atomistic details from coarse-grained-structures

Hi James, Yes, that is possible too. If you need a hand, contact me off-list. Best, Tsjerk On Mar 17, 2016 16:32, "James Starlight" wrote: > btwh dont understand clearly the whole methodology > > for instance If I have coarse'grained system obtained from the > martinize tool consisted of the 1

Re: [gmx-users] query on plotting dynamical quantity

le format has to be a pdb format. However, if > I have a trajectory ( in xtc format) and each frame's 'bfactor' values are > getting updated, then do I need to convert entire xtc files into pdb files > for visualization? > Jagannath > > > On Tue, Mar 8, 2016 at

Re: [gmx-users] Regarding using random seed

and rerun the simulations: > > continuation = no > gen_vel = yes > gen-seed = -1 > > Right? > > > Best Regards, > > *Neha* > > Research Scholar, > Centre for Computational Biology and Bioinformatics, > School of Life Sciences, > Central University of Himac

Re: [gmx-users] Regarding using random seed

t; changes I have to make and in which .mdp file? > > Best Regards, > > *Neha* > > Research Scholar, > Centre for Computational Biology and Bioinformatics, > School of Life Sciences, > Central University of Himachal Pradesh, > > > > > > On Wed, Mar 9,

Re: [gmx-users] Regarding using random seed

Hi Neha, You can perform a simulation first, and then extract configurations, which you simulate with new starting velocities. Alternatively, you can generate a number of different starting structures using elastic-network modeling, like with the ElNemo server. Mind to first energy minimize the re

Re: [gmx-users] query on plotting dynamical quantity

Hi Jagannath, Convert the file to PDB format and write the values to the b-factor field. Most visualization programs can color by b-value. Cheers, Tsjerk On Mar 8, 2016 06:50, "Jagannath Mondal" wrote: > Dear gromacs-users > > I am sorry to write you a visualization-related query. I hope you

  1   2   3   4   5   >